Definitely use prefabs for as much as possible.
I'd also question whether you need to have 50 scenes... I tried that when I started, but the build times were horrendous
You could just have one, detect what level number it's loading, then instantiate the right prefabs for all of you scenery, objects and behaviours.
One tip incase you do have lots of scenes, use String variables when you use the Load Level actions - rather than manually typing your scene name to load. If you change your scene names you won't then have to manually change a lot of references.